# Publications

2018
F. Meng, Jing, Z., Ferreira, R., Ren, P., and Zhang, F., “Investigating the Association Mechanism between Rafoxanide and Povidone,” Langmuir, 2018.
R. Qi, Jing, Z., Liu, C., Piquemal, J. - P., Dalby, K. N., and Ren, P., “Elucidating the Phosphate Binding Mode of PBP: The Critical Effect of Buffer Solution,” The Journal of Physical Chemistry B, 2018.
Z. Jing, Liu, C., Qi, R., and Ren, P., “Many-body effect determines the selectivity for Ca2+ and Mg2+ in proteins,” Proceedings of the National Academy of Sciences, vol. 115, pp. E7495–E7501, 2018.
Z. Jing and Ren, P., “Mechanism of selectivity for magnesium and calcium in proteins,” in ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2018, vol. 255.
J. A. Rackers, Liu, C., Ren, P., and Ponder, J. W., “A physically grounded damped dispersion model with particle mesh Ewald summation,” The Journal of chemical physics, vol. 149, pp. 084115, 2018.
J. A. Rackers, Wang, Z., Lu, C., Laury, M. L., Lagardere, L., Schnieders, M. J., Piquemal, J. - P., Ren, P., and Ponder, J. W., “Tinker 8: software tools for molecular design,” Journal of chemical theory and computation, vol. 14, pp. 5273–5289, 2018.
C. Zhang, Lu, C., Jing, Z., Wu, C., Piquemal, J. - P., Ponder, J. W., and Ren, P., “AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids,” Journal of chemical theory and computation, vol. 14, pp. 2084–2108, 2018.
L. Lagardère, Jolly, L. - H., Lipparini, F., Aviat, F., Stamm, B., Jing, Z. F., Harger, M., Torabifard, H., Cisneros, A. G., Schnieders, M. J., and others,Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields,” Chemical science, vol. 9, pp. 956–972, 2018.
J. Zhao, Wang, G., del Mundo, I. M., McKinney, J. A., Lu, X., Bacolla, A., Boulware, S. B., Zhang, C., Zhang, H., Ren, P., and others,Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes,” Cell reports, vol. 22, pp. 1200–1210, 2018.
2017
M. Harger, Li, D., Wang, Z., Dalby, K., Lagardere, L., Piquemal, J. P., Ponder, J., and Ren, P. Y., “Tinker-OpenMM: Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs,” Journal of Computational Chemistry, vol. 38, pp. 2047-2055, 2017.Abstract
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a similar to 200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. (C) 2017 Wiley Periodicals, Inc.
X. Han, Jing, Z. F., Wu, W., Zou, B., Peng, Z. L., Ren, P. Y., Wikramanayake, A., Lu, Z. M., and Leblanc, R. M., “Biocompatible and blood-brain barrier permeable carbon dots for inhibition of A beta fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862-12866, 2017.Abstract
Amyloid-beta peptide (A beta) fibrillation is pathologically associated with Alzheimer's disease (AD), and this has resulted in the development of an A beta inhibitor which is essential for the treatment of AD. However, the design of potent agents which can target upstream secretases, inhibit A beta toxicity and aggregation, as well as cross the blood-brain barrier remains challenging. In, this research carbon dots for AD treatment were investigated in vitro using experimental and computational methods for the first time. The results presented here demonstrate a novel strategy for the discovery of novel antiamyloidogenic agents for AD treatments.
B. S. Wendel, He, C. F., Qu, M. J., Wu, D., Hernandez, S. M., Ma, K. Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., Ren, P. Y., Chen, K. K., and Jiang, N., “Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature Communications, vol. 8, 2017.Abstract
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (<12 months old) and toddlers (12-47 months old) with 4-8ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.
C. Zhang, Bell, D., Harger, M., and Ren, P., “Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases,” J Chem Theory Comput, 2017.Abstract
Aromatic molecules with pi electrons are commonly involved in chemical and biological recognitions. For example, nucleobases play central roles in DNA/RNA structure and their interactions with proteins. The delocalization of the pi electrons is responsible for the high polarizability of aromatic molecules. In this work, the AMOEBA force field has been developed and applied to 5 regular nucleobases and 12 aromatic molecules. The permanent electrostatic energy is expressed as atomic multipole interactions between atom pairs, and many-body polarization is accounted for by mutually induced atomic dipoles. We have systematically investigated aromatic ring stacking and aromatic-water interactions for nucleobases and aromatic molecules, as well as base-base hydrogen-bonding pair interactions, all at various distances and orientations. van der Waals parameters were determined by comparison to the quantum mechanical interaction energy of these dimers and fine-tuned using condensed phase simulation. By comparing to quantum mechanical calculations, we show that the resulting classical potential is able to accurately describe molecular polarizability, molecular vibrational frequency, and dimer interaction energy of these aromatic systems. Condensed phase properties, including hydration free energy, liquid density, and heat of vaporization, are also in good overall agreement with experimental values. The structures of benzene liquid phase and benzene-water solution were also investigated by simulation and compared with experimental and PDB structure derived statistical results.
F. Aviat, Levitt, A., Stamm, B., Maday, Y., Ren, P., Ponder, J. W., Lagardere, L., and Piquemal, J. P., “Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations,” J Chem Theory Comput, vol. 13, pp. 180-190, 2017.Abstract
We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration ("peek"), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter omega, can be made at almost no cost. This method is denoted by TCG-n(omega). Black-box adaptive methods to find good choices of omega are provided and discussed. Results show that TPCG-3(omega) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(omega) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production algorithm. The T(P)CG-1(omega) level provides less accurate solutions for inhomogeneous systems, but its applicability to well-conditioned problems such as water is remarkable, with only two matrix-vector product evaluations.
Z. Jing, Liu, C., Cheng, S., Qi, R., Walker, B., Piquemal, J. - P., and Ren, P., “Polarizable force fields for biomolecular simulations: Recent advances and applications,” annual review of biophysics, 2017.
X. Han, Jing, Z., Wu, W., Zou, B., Peng, Z., Ren, P., Wikramanayake, A., Lu, Z., and Leblanc, R. M., “Biocompatible and blood–brain barrier permeable carbon dots for inhibition of A$\beta$ fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862–12866, 2017.
S. Deng, Wang, Q., and Ren, P., “Estimating and modeling charge transfer from the SAPT induction energy,” Journal of computational chemistry, vol. 38, pp. 2222–2231, 2017.
B. S. Wendel, He, C., Qu, M., Wu, D., Hernandez, S. M., Ma, K. - Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., and others,Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature communications, vol. 8, pp. 531, 2017.
C. Liu, Qi, R., Wang, Q., Piquemal, J. - P., and Ren, P., “Capturing many-body interactions with classical dipole induction models,” Journal of chemical theory and computation, vol. 13, pp. 2751–2761, 2017.